Downsampling is the process of selecting a limited number of data points/events from a sample or gated population. A new Downsample Gate is created containing the selected subset of events, which can be used like any other gated subset or population node within FlowJo.

Downsampling is often a necessary prerequisite to algorithmic calculations like t-Distributed Stochastic Neighbor Embedding (tSNE), as reducing the number of events fed into an algorithm will decrease calculation speed and provide an output in a reasonable period of time. 

FlowJo v10.1r7 and above use a Plugin mechanism for creating downsample gates. Plugins can be accessed and run through the Plugins menu (Workspace tab –> Populations band).


  • Please see the Installing Plugins page for detailed information on how to obtain and setup FlowJo plugins.
  • The DownSample plugin does not require R.


Basic Operation:

  1. Open FlowJo v10.1r7 or later.
    • If using an earlier version of FlowJo, please download and install the latest release for Mac or Windows, before proceeding. The DownSample plugin is included with the installation package.
  2. Select/highlight a gated population within the samples pane of the FlowJo workspace.
  3. Initiate DownSample from the Plugins menu (Workspace Tab –> Populations Band)                         . Downsample1         DownSample_Plugin__1_1_
  4. Enter the Number of events desired in the downsample gate.
  5. Name the downsample gate (optional) and click OK.

The DownSample plugin will randomly sample events from the selected parent subset and create a new child gate with the user entered name containing those events.


This gate can be used like any other gate in FlowJo, and can be fed into other Plugins, including tSNE, SPADE or FlowMeans.

For more information on installing and running specific Plugins:

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